Like the young intellectuals whose agonies were once a staple of a certain kind of (usually German) coming-of-age novel, Marco Roth grew up in an atmosphere of high culture, liberal values and material comfort. His tribulations, though fascinating, were not the kind we've grown accustomed to from contemporary memoirs. There were no beatings and he became, not a junky, but the co-founder (with Benjamin Kunkel and Chad Harbach) of the celebrated magazine n+1, his generation's Partisan Review.

His father was a scientist, his mother a musician. They lived in a book-filled home on New York's Upper West Side, where Marco, aged eight, lolled on the carpet reading Shakespeare: "I was the definition of 'precocious'." An ancestor had founded Van Heusen shirts, and there was evidently no shortage of money. It wasn't quite on the scale of Buddenbrooks, but among the incidental pleasures of The Scientists is the glimpse of a rarefied subset of New York's intelligentsia, as close to extinction now (unless n+1 has somehow revived it in Brooklyn) as Thomas Mann's merchant princes were in his day.

Deadly illness, as in Mann, is both a cause and symptom of the family's decline. Marco's father, Eugene, was infected with HIV when Marco was a child. He developed full-blown Aids when Marco was 14 and died two years later, in 1993. His explanation was that he had accidentally infected himself with a needle at his medical laboratory. The story enabled him to play the dignified stoic, but it turned out, as Marco discovered many years later, to be almost certainly a lie.

In those early years of the Aids epidemic, even victims who had been "innocently" infected had good reason to keep quiet about it. Eugene claimed he could lose his lab if it were known he had HIV. Perhaps he was right: at any rate, the stigma gave him a good excuse for imposing a regime of strict secrecy on his household, thickening its already humid conservatoire atmosphere with toxic vapours of repression and duplicity, and instilling early habits of guardedness in his only child.

The first third of the book portrays the emotionally convoluted father through the eyes of his never-quite-comprehending son. There is the couch where Eugene taught his son to read, and on which he was later to die. There are the poignant confusions of Marco's inner life: the fantasy of turning himself into a medical superhero in time to cure his father, vacillating with the constantly suppressed urge to ask, "When are you going to die?" There are the silent sessions with the shrink he was sent to after a plate-smashing episode, the fear that his schoolfriends are going to find out about his father's illness, the irresistible compulsion to tell them …

The father, especially, emerges as a figure of novelistic presence and complexity. A little like the old Prince Bolkonsky in War and Peace, his evidently sincere paternal love comes out as coldness or cruelty more often than tenderness. Anything that threatens him with social shame provokes an irrational severity. A minor boyhood peeing accident of Marco's becomes a source of undying resentment. In a fixed attitude of defiance against his own tyrannical father, Eugene decrees a life of enlightened autonomy for his son, unaware of the tyrannical nature of his fiats. "You are a person," he dauntingly instructs the infant Marco (so his mother remembers). "You will hate me just as I hated my father," he informs the boy at eight. "You'll be disappointed," he tells him when Marco decides to study at Oberlin rather than his own alma mater, Columbia.

This gesture of independence, far from pleasing Eugene, causes him to threaten Marco with disinheritance, which creates a rift between them that lasts almost until the father's death. The tersely written death scene derives much of its disquieting power from the reverberations of the unfinished business between father and son.

After this section, which reads like an extremely well-wrought novella, the book largely shifts register from the dramatic to the analytic. It is less gripping to read, though there is still an element of suspense (it is clear by now that the father is hiding something large from his family). With his main character dead, what remains for Roth is to decipher him from the vantage point of his own painfully acquired maturity.

He begins by looking at his father's effect on his own psyche, presenting himself as a study in indecisiveness, stalled ambition, sexual vagueness, and general ineffectuality (not unlike the character in Benjamin Kunkel's novel Indecision). Falling under the enchantment of Deconstruction, he drifts from college to college, city to city, menage to menage – Columbia, Paris (where he studies briefly with Jacques Derrida), Oxford, Yale; a third leg limping along with various couples of his acquaintance, or floating in and out of evanescent liaisons of his own. These parts stretch one's patience a little, but they do substantiate the idea of some deep damage having been done. Still, the precise nature of the link between the father's long demise and the son's "habit of failure" remains mysterious for some time.

And then the likely true cause of his father's infection confronts Marco, unexpectedly and unceremoniously, in a new book by his aunt, the writer Anne Roiphe (mother of Katie; this is a serious literary dynasty here). Resistant at first, he finds the suggestion reluctantly corroborated by other people. The issue for Marco, once the shock settles, isn't that his father was gay (or bisexual), but that he lived a lie and imprisoned his family in that lie.

Naturally enough, in a story about a tainted emotional legacy and a virus that invades a person's DNA, Roth is hyperalert to the possibility of creative slippage between literal and metaphorical inheritance. Taking his cue from the antiviral drugs his father was given – "reverse transcriptase inhibitors" – he embarks on his own "reverse transcription", rereading the novels his father pressed on him long ago, in an effort to deconstruct what he punningly calls his father's "textuality" (and, of course, his own). He does this gracefully and without jargon, scouring Tonio Kroger, Oblomov and Fathers and Sons for clues to what his father was possibly trying to tell him all along. It may not furnish quite the sensational ending the opening seems to promise, and some readers will find it too inward and bookish. But it is appealingly honest, and in its own way wrestles with the large conflicts its talented author has confronted, and survived.